Prenatal maternal psychological stress is common in pregnant women. Heart rate variability (HRV) has recently become considered to be a potentially reliable stress biomarker in adults. Methods:In the current study, we evaluated ultra-short-term HRV (1-minute measurement) as a stress indicator among pregnant women (N = 230) by examining the association between HRV parameters and self-reported prenatal maternal psychological stress (emotional distress, and anxiety). Results: Prenatal emotional distress was associated with a lower root mean square of successive differences between normal heartbeats (RMSSD), pNN50, SDNN Index, and low-frequency power (LF) among healthy pregnant women participants. In addition, prenatal anxiety was related to a lower-than-normal high-frequency power (HF) and elevated LF/HF values. For high-risk pregnant women (with reported scores greater than or equal to the 90th percentile), prenatal emotional distress and anxiety were not significantly correlated with any HRV indicators. Conclusions: Low HRV (associated with reduced parasympathetic activity) can serve as an efficient biomarker for psychological stress in healthy pregnant women. However, the HRV indicators in pregnant women with a high risk of psychological stress problems may be affected by other mental or physical problems, thus decreasing the biomarker’s efficiency in predicting their prenatal psychological stress.